Genome of a husavirus from Southern Brazil

New viruses of the Picornavirales order have been discovered with the increase in the number of sequences obtained by high-throughput sequencing, as well as human stoolassociated RNA virus (husavirus [HuV]), found in human stool samples. However, there is much to be clarified about HuV. Its cellular host, evolutionary history, and other biological characteristics are still unknown. Therefore, samples collected from human beings and environmental samples in a watershed in Southern Brazil were processed for the metagenomic library. Upon metagenomic analysis, we identified a HuV (husavirus LMM_67754 OP019707) genome with 8,846 bp, which was reported for the first time in Southern Brazil. The new genome presents only 37% of nucleotide identity with Brazilian strains and more than 90% with genomes from China, Vietnam, Venezuela, and the Netherlands. The HuV phylogeny presents significant differences among genomes, probably because multiple introductions of the virus may have occurred. Many questions still need to be answered about HuV. Therefore, more sequences and studies on this virus are necessary to improve the comprehension of the unknown origin of Picornavirales

Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2

Multiple variants of the Severe Acute Respiratory Syndrome coronavirus 2 virus (SARS-CoV-2) have been constantly reported across the world. The B.1.1.28 lineage has been evolving in Brazil since February 2020 and originated the P.1 variant of concern (VOC), recently named as the Gamma variant by the newly WHO nomenclature proposal, and P.2 as a variant of interest (VOI). Here we describe an early case of P.1 primary infection in Southern Brazil in late November 2020, soon after the emergence of the variant in Manaus, Northern Brazil. The same male patient was reinfected by another B.1.1.28 variant, namely P.2, in March, 2021. The genomic analysis confirmed genetically significant differences between the two viruses recovered in both infections, the P.1 lineage in the first episode and P.2 in the reinfection. Due the very early detection of P.1, we have also investigated the circulation of P.1 in the same region by differential RT-qPCR, showing that this was an isolated case of P.1 at the time of detection, and this variant has disseminated and became prominent from late January to the end of March, 2021. SARS-CoV-2 recent reports of reinfection have raised critical questions on whether and how well a first infection protects against reinfection

Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Background: Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%). Results: We provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologicallyrelated clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions. Conclusions: Our data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19

Evaluation of the Gravataí River sediment quality (Rio Grande do Sul- Brazil) using Daphnia magna (Straus, 1820) as the test-organism for toxicity assays Avaliação da qualidade dos sedimentos do rio Gravataí (Rio Grande do Sul - Brasil) a partir de testes de toxicidade utilizando Daphnia magna (Straus, 1820) como organismo-teste

AIM: Persistent pollutants released to riverbeds return to the trophic system, damaging living organisms thereof. Ecotoxicological assays express the effect of environmental interactions with organisms found there. Assays were performed with microcrustacean Daphnia magna (Straus, 1820) in sediment samples, from the headwaters to the mouth, in order to evaluate the Gravataí River quality; METHODS: Bottom sediment was used to evaluate the responses of cladocerans to environmental changes in 15 samples collected between Jan./06 and May/09. The microcrustaceans were submitted to stress for 21 days from birth (2-26 hours old). Duncan Test, percentage survival, reproduction and Spearman Correlation were used to evaluate the quality of the sites; RESULTS: Duncan Test showed a significant difference (p < 0.05) in reproduction in 14 of the 15 samplings, and chronic action was more constant (88%) than the acute one (23%). Changes in survival and reproduction related to season or rainfall regime were only observed on a few occasions. The two sites located close to the mouth presented a Spearman Correlation (p < 0.01) for survival and reproduction. There were changes in some samplings in the headwaters as a result of sewage discharges in the area; CONCLUSIONS: Fluctuating responses were observed in this river due to anthropic contaminants, slow flux and current reflux.<br>OBJETIVO: Poluentes persistentes lançados no leito dos rios retornam ao sistema trófico danificando os organismos que o integram. Os ensaios ecotoxicológicos expressam o efeito das interações ambientais com os organismos ali presentes. Visando avaliar a qualidade do rio Gravataí foram realizados ensaios com o microcrustáceo Daphnia magna (Straus, 1820), em amostras do sedimento, da nascente até a foz; MÉTODOS: Sedimento de fundo foi utilizado na avaliação das respostas dos cladóceros às alterações ambientais de 15 amostras coletadas entre Jan./06 e Maio/09. Os microcrustáceos foram colocados em situação de estresse durante 21 dias desde o início de suas vidas (2-26 horas). O Teste de Duncan, percentual de sobrevivência, reprodução e Correlação de Spearman foram utilizados para avaliar a qualidade dos locais; RESULTADOS: O Teste de Duncan mostrou diferença significativa (p < 0,05) na reprodução em 14 das 15 amostragens, sendo a ação crônica mais constante (88%) que a aguda (23%). Somente em algumas ocasiões foram observadas alterações na sobrevivência e na reprodução relacionadas à estação climática ou regime de chuvas. Os dois locais situados próximos a foz apresentaram Correlação de Spermann (p < 0,01) para sobrevivência e reprodução. Aqueles situados na nascente mostraram alterações em algumas amostragens em decorrência dos lançamentos de esgotos na área; CONCLUSÕES: Flutuações de respostas foram observadas neste rio devido aos contaminantes de origem antrópica, fluxo lento e refluxo de correntes

Bioassay using Daphnia magna Straus, 1820 to evaluate the sediment of Ca\ued River (Rio Grande do Sul, Brazil)

AIM: The Caí River is one of the five that form the Guaiba Lake Hydrographic Basin. It is used for public water supply in the capital of Rio Grande do Sul; METHODS: Sediment samples for toxicity test (21 days) with Daphnia magna were taken from four sites between the middle and upper reaches in this river from Mar./05 to June/09. Their quality is described based on the survival and reproduction responses of 440 test-organisms from the beginning of their lives (2-26 hours). Percentage survival, mean and total reproduction were calculated for this evaluation. Spearman correlation and Duncan Test were used to compare reproduction between sites and variation of this parameter statistically over time. Bacteriological, physical and chemical parameters in water samples collected during the period of the study were considered; RESULTS: Acute toxicity was observed in 18% of the samples and chronic toxicity in 95%, indicating the presence of small doses of environmental aggressors. Mortality and reproduction did not always follow the same trend, and it became clear that the reproductive activity was more sensitive when compared using contaminated samples. Duncan Test showed up to four clusters at sites Ca070, Ca092 and Ca245, indicating reproduction variation. A pattern of monthly rainfall distribution was not observed, nor was there a correlation between survival, reproduction and rainfall; CONCLUSIONS: Presence of low concentrations of xenobiotics was confirmed by physical, chemical, bacteriological and metal responses in water samples, besides a small effect on survival and constant change in reproductive activity in the organisms exposed to sediment samples. Long duration assays are more appropriate to evaluate environmental samples, since usually changes in ecosystem quality are tenuous and not detected by short tests. Caí River quality has improved, but further studies are needed to confirm this trend, and to follow the history of the area with a more detailed definition of the course characteristics and the most fragile sites in the region

Diversity of Omicron sublineages and clinical characteristics in hospitalized patients in the southernmost state of Brazil

Abstract Background Omicron has become the dominant variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since first reported in November 2021. From the initially detected Wuhan lineage, sublineages BA.2, BA.4, BA.5, BQ, XAG, and XBB have emerged over time and are dominant in many countries. Therefore, the aim is to evaluate which variants are circulating and the clinical characteristics of inpatients infected with the Omicron variant. Methods This retrospective cohort study selected hospitalized patients admitted with respiratory symptoms to a hospital in the state of Rio Grande do Sul, Brazil, between June and July 2022. SARS-CoV-2 results were analyzed together with clinical outcomes and vaccination status. A viral genome library was prepared and forwarded to the Illumina MiSeq Platform for sequencing. Results In total, 37 genomes were sequenced. Concerning the Omicron sublineages, our study detected: BA.1 (21 K), BA.2 (21 L), BA.4 (22A), BA.5 (22B), BA.2.12.1 (22C), BQ.1 (22E), XBB (22F), and XAG recombinant. Omicron BA.5 (30%), BA.2 (19%), and BQ.1 (19%) were the most frequent sublineages, respectively. In total, 38% of patients present hypertension, and the most common symptoms were coughing (62%). Analyzing the COVID-19 vaccination, 30% of patients were fully vaccinated, 49% had a partial vaccination status, and 21% were unvaccinated (no dose). Conclusions BA.5 was the most prevalent sublineage in our study and surpassed the predominance of BA.2, as reported by the national genomic surveillance program. BQ.1 was diagnosed earlier in this study than it was officially reported in the state. Current data have demonstrated that the Omicron variant causes less severe infections, with the high rate of transmissibility and mutational landscape causing the rapid emergence of new sublineages

Functionalized Surfaces as a Tool for Virus Sensing: A Demonstration of Human mastadenovirus Detection in Environmental Waters

The main goal of this study was to apply magnetic bead surface functionalization in the form of immunomagnetic separation (IMS) combined with real-time polymerase chain reaction (qPCR) (IMS-qPCR) to detect Human mastadenovirus species C (HAdV-C) and F (HAdV-F) in water samples. The technique efficiency was compared to a nonfunctionalized method (ultracentrifugation) followed by laboratory detection. Tests were carried out to standardize IMS parameters followed by tests on 15 water samples concentrated by IMS and ultracentrifugation. Microscopic analyses detected a successful beads&ndash;antibody attachment. HAdV was detected up to dilutions of 10&minus;6 by IMS-qPCR, and samples concentrated by IMS were able to infect cell cultures. In water samples, HAdV-C was detected in 60% (monoclonal) and 47% (polyclonal) by IMS-qPCR, while 13% of samples concentrated by ultracentrifugation gave a positive result. HAdV-F was positive in 27% of samples by IMS-qPCR (polyclonal) and ultracentrifugation and 20% by IMS-qPCR (monoclonal). The rate of detection varied from 4.55 &times; 102 to 5.83 &times; 106 genomic copies/L for IMS-qPCR and from 2.00 &times; 102 to 2.11 &times; 103 GC/L for ultracentrifugation. IMS showed to be a more effective concentration technique for HAdV than ultracentrifugation, improving the assessment of infectious HAdV in water resources

Additional file 1 of Diversity of Omicron sublineages and clinical characteristics in hospitalized patients in the southernmost state of Brazil

Supplementary Material 1

<b>Supplementary Figure</b>

Maximum-likelihood tree constructed using RAxML v8.0 using the complete coding sequences of (A) PB2 gene, (B) PB1, (C) PA, (D) NP, (E) MP, and (F) NS gene segments. The red taxa label indicates the virus sequenced in this study. Node labels indicate the bootstrap value (%).</p